[gmx-users] Missing frames in trajectory?

[Mark Abraham]

Possibly. There were appending bugs fixed during the 4.5.x series.
There are also bugs in file systems that prevent appending working
properly in all cases. Check out the release notes, consider updating,
or using -noappend.

Mark

On Tue, Jul 2, 2013 at 2:41 PM, Humphrey Morhenn
<Humphrey.Morhenn at frm2.tum.de> wrote:
> On 07/02/2013 01:34 PM, Justin Lemkul wrote:
>> On Tue, Jul 2, 2013 at 7:26 AM, Humphrey Morhenn <
>> Humphrey.Morhenn at frm2.tum.de> wrote:
>>
>>> Dear users,
>>>
>>> there seem to be alot of frames missing in my .trr trajectory file and I
>>> wonder if anyone knows how to recover the (hopefully not lost) information.
>>>
>>> tinit                    = 0
>>> dt                       = 0.001
>>> nsteps                   = 120000000
>>> nstxout                  = 1000000
>>>
>>> When I e.g. run trjconv -pbc mol -f (.trr) -s (.tpr) -o (.trr), it says:
>>> Reading frame  0 time 77000.000
>>> Reading frame 30 time 107000.000 -> frame 30 time 107000.000
>>>
>>> What happened to the frames <77ns and >107ns?
>>>
>>>
>> When running trjconv, trjcat, etc, Gromacs reports the frame it is reading
>> and then over-writes the line as it progresses through the trajectory. You
>> have 30 frames spanning 30 ns, which is exactly what your .mdp file
>> specifies.  You haven't posted any information (previous protocol,
>> remainder of .mdp, etc) that would indicate why the trajectory starts at 77
>> ns.
>>
>> -Justin
>>
>
> Ok, I checked the trajectory with gmxcheck, and indeed the file ends at
> 120ns. But still, there are only 44 frames in the file, instead of 121
> as specified in the .mdp file.
>
> The .trr file was not modified after the simulation. The simulation
> itself was performed on a cluster with v4.5.4, using the options
> -npme -1 -s (.tpr) -deffnm () -cpi -append for ALL consequtive runs. The
> energy and log files are both complete. It seems like the trajectory
> file was not appended, but overwritten instead?
>
> The input .mdp file for grompp is
> constraints = none
> integrator = md
> dt = 0.001 ; ps !
> nsteps = 120000000
> nstcomm = 1
> nstenergy = 100
> nstcalcenergy = 10
> nstxout = 1000000
> nstvout = 0
> nstfout = 0
> nstlist = 10
> ns_type = grid
> rlist = 1.0
> coulombtype = PME
> rcoulomb = 1.0
> rvdw = 2.0
> fourierspacing = 0.15
> optimize_fft = yes
> Tcoupl = Nose-Hoover
> tau_t = 4.0
> ref_t = 509
> Pcoupl = Parrinello-Rahman
> pcoupltype = isotropic
> tau_p = 20.0
> compressibility = 4.5e-5
> ref_p = 1.01325
>
> Regards,
> Humphrey
>
>
> --
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